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British Airways' sale of BA Connect to Flybe in 2007 did not include the London City Airport operations and its associated fleet of ten Avro RJ100 regional jet aircraft. This led to British Airways' decision to resurrect erstwhile Gatwick-based CityFlyer Express (which BA had integrated into its Gatwick mainline short-haul operation in 2001, following the acquisition of CityFlyer Express in 1999) as a new wholly owned subsidiary to take over this operation, as of March 2007[update]. BA CityFlyer was awarded an Air Operators Certificate on 8 February 2007, and started operations on 25 March 2007.[6]

In February 2016, BA Cityflyer announced that it would commence operating flights from London-Stansted in May 2016. In January and February 2017, they announced that they would commence summer seasonal services from Manchester, Bristol, Edinburgh, Dublin and Birmingham to a variety of destinations in Spain, Italy, Greece and France. This marks the return of BA to the regions after an absence of nearly 10 years. Flights will also operate in the summer between London City and Manchester, operating with Embraer 190 aircraft.

BA Cityflyer also lease a small number of aircraft for other airlines. These aircraft are operated and crewed by the third party airline on behalf of BA Cityflyer. As of November 2018, BA Cityflyer lease the following aircraft

On 13 February 2009, BA CityFlyer Flight 8456 (an Avro RJ100, registered G-BXAR, flying from Amsterdam) suffered a nose-gear collapse whilst landing at London City Airport. None of the 67 passengers or five crew members was seriously injured in the incident, but three passengers suffered minor injuries, two of whom were kept in hospital overnight. After a normal approach the nose landing-gear fractured as it was lowered onto the runway, due to the presence of a fatigue-crack in the upper internal bore of the landing-gear main fitting.

It was found that the crack had formed as a result of poor surface finish during manufacture, and the incomplete embodiment of a manufacturer's service bulletin, which the landing-gear maintenance records showed as being implemented at its last overhaul in June 2006.[14][15] The aircraft was damaged beyond economic repair, and was written-off by insurers in May 2009.[16]